Well...I think for me it's really a case of characters I dislike when they are written in a certain way. Mara Jade and Wedge Antilles are some of my favorite characters in all of literature - but when they are written badly (see also: Mara as written by Denning, Wedge as written by Keyes) they are almost worse than characters who annoy me in principle because they are supposed to be so much more.

Similarly, characters who I don't really like can be written extremely well by other authors - such as Zsinj by Allston after the very silly Wolverton Zsinj.

Jaina. Her whole 'don't get too close to me' persona in NJO drove me nuts. If you continue to drive people away, eventually people will stop trying. She didn't even try to console one of her best friends in 'Dark Journey'. Tenel Ka's mother dies, the love of her life has been taken prisoner, she's forced to assume the role that she never wanted, and Jaina does nothing to help except wallow in her own misery.

Her and Zekk become Joiners, encouraging the Killiks (and the Dark Nest) to continue to antagonize the Chiss, and do they get punished? No. Tahiri, Tesar, and Lowbacca get sent to Dagobah, but Jaina and Zekk are left alone. Jaina got a free pass with everything. If I were Jag, I'd have dumped her like a bad habit.

LFL missed the boat, Jaina turning dark would have been much easier to write; she was already a self-absorbed punk.

Maybe an unpopular opinion, but Tahiri always annoyed me. I'm sure if someone wrote some good meta on her I could be convinced otherwise, but the way she is in the books just completely rubs me the wrong way. There are others that I dislike, but I'd have to look at some character lists or something because Tahiri's the only one who comes to mind.

On-Topic: DE Palpy annoys me...yes, not technically an EU character, but he might as well be with the absurd power levels. I swear, it was like reading some cheap fanboys view of how Palpy should be...